1LTX

Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

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Literature

Structure of Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase

Pylypenko, O., Rak, A., Reents, R., Niculae, A., Sidorovitch, V., Cioaca, M.D., Bessolitsyna, E., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.

(2003) Mol Cell 11: 483-494

  • DOI: 10.1016/s1097-2765(03)00044-3
  • Primary Citation of Related Structures:  
    1LTX

  • PubMed Abstract: 

    • Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2 ...

    Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies.

    Related Citations: 
    • Crystallization and Preliminary X-ray Diffraction Analysis of the Rab Escort Protein-1 in Complex with Rab Geranylgeranyltransferase
      Rak, A., Reents, R., Pylypenko, O., Niculae, A., Sidorovitch, V., Thoma, N.H., Waldmann, H., Schlichting, I., Goody, R.S., Alexandrov, K.
      (2001) J Struct Biol 136: 158
    Organizational Affiliation: 

    Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNITA567Rattus norvegicusMutation(s): 0 
Gene Names: Rabggta, Ggta
EC: 2.5.1 (PDB Primary Data), 2.5.1.60 (UniProt)
UniProt
Find proteins for Q08602 (Rattus norvegicus)
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UniProt GroupQ08602
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAB GERANYLGERANYLTRANSFERASE BETA SUBUNITB331Rattus norvegicusMutation(s): 0 
Gene Names: Rabggtb, Ggtb
EC: 2.5.1 (PDB Primary Data), 2.5.1.60 (UniProt)
UniProt
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UniProt GroupQ08603
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Rab Escort Protein 1C [auth R]650Rattus norvegicusMutation(s): 3 
Gene Names: Chm, Rep1
UniProt
Find proteins for P37727 (Rattus norvegicus)
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UniProt GroupP37727
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AAAAD [auth P]4N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAR
Query on FAR
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G [auth P]FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N		 Ligand Interaction
ZN
Query on ZN
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E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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F [auth R]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.7α = 90
b = 197.3β = 112.8
c = 85.3γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations